I always head-canon that the transporter pad auto adds .02mm to the Z-Axis of anything that beams in. Just far enough enough that a person won’t really feel it, and objects don’t rattle or tip from the tiny drop, but not too far so it’s not as jarring. Of course a good transport operator can override this, to make an even “smoother” landing. If the tech can reassemble molecules, then why not have an accuracy of microns rather then millimeters? No chance of interphasing matter, if it never overlaps.
I find it fun to play my characters with various symptoms of my own neurodivergence. And the occasional NPC in a game I’m DMing will stand out this way as well. I find it adds variety and makes things more real and interesting. A great way I found to include neurodivergence that can have game mechanics tied to it is Limitless Heroics by Wyrmworks, so you could check that out.
Tool use? Any examples of this, cause that sounds like it would be cool to learn about.